This invention relates to nucleic acid and amino acid sequences of human transferase proteins and to the use of these sequences in the diagnosis, treatment, and prevention of cancer, developmental disorders, gastrointestinal disorders, genetic disorders, immunological disorders, neurological disorders, reproductive disorders, and smooth muscle disorders.
Transferase Proteins
Transferases are enzymes that catalyze the transfer of molecular groups from a donor to an aceeptor molecule. The reaction may involve an oxidation, reduction, or cleavage of covalent bonds and is often specific to a substrate or to particular sites on a type of substrate. Transferase proteins participate in reactions essential to such functions as synthesis and degradation of cell components, and regulation of cell functions, including cell signaling, cell proliferation, inflammation, apoptosis, secretion and excretion. Transferases are involved in key steps in disease processes involving these functions. These enzymes are frequently classified according to the type of group transferred. For example, methyl transferases transfer one-carbon methyl groups, amino transferases transfer nitrogenous amino groups, and similarly denominated enzymes transfer aldehyde or ketone, acyl, glycosyl, alkyl or aryl, isoprenyl, saccharyl, phosphorous-containing, sulfur-containing, or selenium-containing groups, as well as small enzymatic groups such as Coenzyme A.
One example of a glycosyl transferase is O-linked N-acetylglucosamine (O-GlcNAc) transferase, an enzyme that catalyzes the reaction of monosaccharide N-acetylglucosamine linking to the hydroxyl group of a serine or threonine residue. O-GlcNAc and N-acetyl-xcex2-D-glucosaminidase (O-GlcNAcase), regulate the attachment and removal, respectively, of O-GlcNAc from proteins in a manner analagous to regulation of protein phosphorylation by kinases and phosphotases. O-GlcNAc transferase has been localized primarily in the nucleus and the cytosol of cells and has been shown to play a role in several cellular systems such as transcription, nuclear transport, and cytoskeletal organization. O-GlcNAc transferase is a heterodimer consisting of two catalytic 110-kDa (p110) subunits and one 78-kDa (p78) subunit. The gene encoding this enzyme is highly conserved. The amino terminus of the p110 subunit has homology to the tetratricopeptide repeat (TPR) motif while the carboxyl terminus has no significant homology (Kreppel, L. K. et al. (1997) J. Biol. Chem. 272:9308-9315). Proteins containing the TPR motif interact through this TPR domain to form regulatory complexes. TPR motifs are believed to play a role in modulation of cellular processes such as cell cycle, transcription, and protein transport (Das, A. K. et al. (1998) EMBO J 17:1192-1199).
The enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a purine salvage enzyme that catalyzes the conversion of hypoxanthine and guanine to their respective mononucleotides. HGPRT is ubiquitous, is known as a xe2x80x98housekeepingxe2x80x99 gene, and is frequently used as an internal control for reverse transcriptase polymerase chain reactions. There is a serine-tyrosine dipeptide that is conserved among all members of the HGPRT family and is essential for the phosphoribosylation of purine bases(Jardim, A. and Ullman, B. (1997) J. Biol. Chem. 272:8967-8973). A partial deficiency of HGPRT can lead to overproduction of uric acid, causing a severe form of gout. An absence of HGPRT causes Lesch-Nyhan syndrome, characterized by hyperuricaemia, mental retardation, choreoathetosis, and compulsive self-mutilation (Sculley, D. G. et al. (1992) Hum Genet 90:195-207).
Polyprenyl transferases catalyze the addition of polyprenyl groups to molecules. For example, the enzyme 1,4-dihydroxy-2-napthoate octaprenyltransferase catalyzes the conversion of the soluble 1,4-dihydroxy-2-napthoic acid (DHNA) to the membrane-bound demethylmenaquinone by attaching a 40-C side chain to DHNA, a key step in the biosynthesis of menaquinone (vitamin K2). This octaprenyltransferase is a membrane protein in Escherichia coli that is necessary for the synthesis of menaquinone (Suvarna, K. et al. (1998) J. Bacteriol. 180:2782-2787). Quinones, in many cases, take part in the oxidation-reduction cycles essential to living organisms (Morrison, R. T. and Boyd, R. N. (1987) Organic Chemistry, Allyn and Bacon, Inc., Newton, Mass., pp. 1092-1093). Other octaprenyltransferase have been shown to allow the synthesis of quinones under anaerobic conditions and, therefore, may play a role in anaerobic metabolism (Alexander, K. and Young, I. G. (1978) Biochemistry 17:4750-4755).
The synthesis of 3xe2x80x2-phosphoadenosine-5xe2x80x2-phosphosulfate (PAPS) requires two enzymes, adenosine triphosphate (ATP) sulfurylase and adenosine 5xe2x80x2-phosphosulfate (APS) kinase. ATP sulfurylase catalyzes the formation of APS from ATP and free sulfate. APS kinase phosphorylates APS to produce PAPS, the sole source of donor sulfate in higher organisms. In bacteria, fungi, yeast, and plants, these two enzymes are separate polypeptides. In animals, ATP sulfurylase and APS kinase are present in a single protein. The bifunctional enzyme found in mammals shows extensive homology to known sequences of both ATP sulfurylases and APS kinases. APS kinase peptide sequences are well conserved and contain an ATP-GTP binding motif (P-loop) flanked by cysteine residues and a PAPS-dependent enzyme motif. ATP sulfurylase peptide sequences have a PP-motif found in ATP sulfurylases and PAPS reductases (Rosenthal, E. and Leustek, T. (I995) Gene 165:243-248; Li, H. et al. (1995) J. Biol. Chem. 270:29453-29459; Deyrup, A. T. et al. (1998) J. Biol. Chem. 273:9450-9456; Bork, P. and Koonin, E. V. (1994) Proteins 20:347-355).
The enzyme phosphatidylethanolamine N-methyltransferase (PEMT) catalyzes the methylation of phosphatidylethanolamine. Hepatocytes in the liver synthesize phosphatidylcholine (PC) by stepwise methylation of phosphatidylethanolamine and have abundant activity for PEMT. Other cells and tissues express minimal activities for PEMT. All mammalian cells, including hepatocytes, synthesize PC from choline via the CDP-choline pathway. Evidence suggests that one function of hepatic PEMT is to maintain PC synthesis and generate choline when dietary supply of choline is insufficient, as occurs during pregnancy, lactation, or starvation (Walkey, C. J. et al. (1998) J. Biol. Chem. 273:27043-27046). Forms of PEMT may also play a role in hepatocyte proliferation and liver cancer (Walkey, C. J. et al. (1999) Biochim. Biophys. Acta 1436:405-412). In the brain, decreased PEMT activity has been associated with Alzheimer""s disease (Guan, Z. Z. et al. (1999) Neurochem. Int. 34:41-47).
Sulfotransferase enzymes catalyze the transfer of sulfur-containing groups to molecules. For example, HNK-1 sulfotransferase (HNK-1ST) forms the HNK-1 carbohydrate epitope by adding a sulfate group to glycoproteins and glycolipids. The HNK-1 epitope was discovered by an antibody against human natural killer cells and is found in neural adhesion molecules, including N-CAM and myelin-associate glycoprotein. The HNK-1 carbohydrate epitope was recognized to have functional significance as an auto-antigen involved in peripheral demyelinative neuropathy. The HNK-1ST is a type II membrane protein with a consensus sequence shared by Golgi-associated sulfotransferases. The human and rat HNK-1STs share 90% homology in amino acid sequence. Human HNK-1ST was predominantly detected in fetal brain and in adult brain, testis, and ovary. (See Ong, E. et al. (1998) J. Biol. Chem. 273:5190-5195.)
Camnitine palmitoyitransferase I (CPT I) is an enzyme that catalyzes the transfer of fatty acyl groups from coenzyme A to carnitine, the rate-determining step in mitochondrial fatty acid xcex2-oxidation (a major source of energy production in the cell). CPT I has two structural genes (xcex1 and xcex2) that are differentially expressed in tissues that utilize fatty, acids as fuel. The xcex1 structure is expressed most highly in the liver, pancreatic xcex2 cells, and heart. The xcex2 structural gene of CPT I is predominately expressed in skeletal muscle, adipose tissue, heart, and testis (Yu, G. S. et al. (1998) J. Biol. Chem. 273:32901-32909). CPT I deficiency is a life-threatening disorder that appears to be treatable with medium-chain triglycerides. The disorder first presents, between 8 and 18 months, with Reye syndrome-like episodes associated with fasting due to viral infection or diarrhea. Coma, seizures, hepatomegaly, and hypoketotic hypoglycemia characterize these episodes. Persistent neurological defects are common (Online Mendelian Inheritance in Man entry #255120; ExPASy Enzyme:EC 2.3.1.21).
The enzyme glycine N-methyltransferase catalyzes the transfer of the methyl group from S-adenosyimethionine to glycine to form S-adenosylhomocteine and sarcosine. Glycine N-methyltransferase is a tetramer of identical subunits, has a nucloetide binding region, and is localized in the liver. Amino acid sequence homology is found between glycine N-methlytransferases from rat, rabbit, pig, and human livers. Glycine N-methyltransferase can exist as a dimer which binds polycyclic aromatic hydrocarbons (PAHs) and acts as a transcriptional activator (Ogawa, H. et al. (1998) Int. J. Biochem. Cell Biol. 30:13-26; Bhat, R. and Bresnick, E. (1997) J. Biol. Chem. 272:21221-21226).
Myristoyl CoA:protein N-myristoyl-transferase
N-acylation with the 14-carbon fatty acid, myristate is found on the amino groups of N-terminal glycines of a number of proteins that are essential to normal cell functioning and/or are potential therapeutic targets of disease. Examples of such proteins include subunits of heterotrimeric G proteins, GTP-binding arfl, human immunodeficiency virus gag and nef proteins, myristolated alanine-rich C kinase substrate (MARCKS), the protein phosphatase calcineurin B, the pp60src protein tyrosine kinase, the retinal calcium-binding recoverin, the caveolae-associated endothelial nitric oxide synthase, the catalytic subunit of cAMP-dependent protein kinase, and mitochondria-associated cytochrome b5 reductase. (Glover, C. J. et al. (1997) J. Biol. Chem. 272:28680-28689.) N-myristoylated proteins ate associated with a variety of organelles with the myristate moiety required for such diverse functions as specific protein-protein or protein-lipid interactions, ligand-induced protein conformnational changes, and correct subcellular targeting.
Protein myristoylation occurs almost exclusively cotranslationally during protein synthesis of the first 100 amino acids. The reaction is catalyzed by the enzyme myristoyl CoA:protein N-myristoyl-transferase (NMT) 1 (EC 2.3.1.97). (Towler, D. A. et al. (1987) Proc. Natl. Acad. Sci. 84:2708-2712.) Immunofluorescence microscopy reveals NMT to be distributed uniformly throughout the cytoplasm of yeast and mammalian cells. This finding, plus evidence that N-myristoylation occurs on nascent polypeptides bound to free polyribosomes, establish that NMT is physically localized and functionally active in the cell cytoplasm. (Wilcox, C. et al. (1987) Science 238:1275-1278.)
Protein N-myristoylation appears to be a tightly regulated process involving i) the coordinated participation of several different enzvmes/proteins, e.g. N-methionylaminopeptidase, fatty acid synthetase, long chain acyl-CoA synthetase, acyl-CoA-binding proteins; ii) access of NMT to pools of myristoyl-CoA substrate; and iii) N-myristoyiation of nascent polypeptide substrates during protein synthesis to avoid potential interfering reactions such as N-acetylation and polypeptide folding. The ability of NMT to function in regulated N-myristoylation has implied the existence of mechanisms designed to ensure targeting of NMT to the appropriate protein synthesis machinery. These mechanisms may involve interactions with other cooperating components that facilitate the recognition and efficient N-myristoylation of the rapidly growing polypeptide substrates. (Glover, et al. supra.) Protein N-myristoylation activity may be a chemotherapeutic target for cancer, infectious diseases, and immune disorders. Antagonists of NMT may reduce posttranslational myristoylation of oncoproteins and other growth-activating cellular proteins. (Felsted, R. L. et al., (1995) J. Natl. Cancer Inst. 87:1571-1573; Furuishi, K. et al., (1997) Biochem. Biophys. Res. Comm. 237:504-511.)
Mannose-1-phosphate guanvitransferase
Many secretory proteins and membrane proteins are glycosylated proteins that have covalently attached carbohydrate chains, or oligosaccharides. Some of these glycoproteins have only one or a few carbohydrate groups while others have numerous oligosaccharide side chains, which may be linear or branched. The sugar residues of many plasma membrane glycoproteins orient these proteins in membranes. Sugar residues of glycoproteins are hydrophilic and strongly prefer to be located near the aqueous or extracellular surface rather than the hydrocarbon core of the plasma membrane. Because there is a high energy barrier to the rotation of a glycoprotein from one side of the membrane to the other, the carbohydrate groups of membrane glycoproteins help to maintain the asymmetric character of biological membranes. One of the best-characterized glycoproteins is glycophorin, a protein found in the membrane of red blood cells. Many soluble glycoproteins are known as well, including carrier proteins, antibodies, and many of the proteins contained in lysosomes. Carbohydrate groups of plasma membrane glycoproteins play a major role in cell-cell recognition. Oligosaccharides are involved in many inflammatory processes and may also provide targets for tumor immunotherapy.
Glycoproteins are often linked to their oligosaccharides through asparagine (N) residues. These N-linked oligosaccharides are very diverse, but the many pathways by which they all form have a common first step. A 14 residue core oligosaccharide, containing two N-acetylglucosamine, nine mannose, and three glucose residues, is transferred from a dolichol phosphate donor molecule to certain N residues on the proteins (reviewed in Lehninger, A. L. et al. (1993) Principles of Biochemistry, Worth Publishers, New York, N.Y., pp. 931). Glycosylation is the most extensive of all post-translational modifications in proteins and is essential for the secretion, antigenicity, and clearance of glycoproteins.
A variety of enzymes which are involved in sugar metabolism participate directly or iridirectly in glycosylation, such as certain pyrophosphorylases. ADP-glucose pyrophosphorylases play an important role in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants. Specifically, ADP-glucose pyrophosphorylases catalyze the synthesis of the activated glucosyl donor, ADP-glucose, from glucose-1-phosphate and ATP. ADP-glucose pyrophosphorylases are tetrameric, allosterically regulated enzymes. There are a number of conserved regions in the sequence of bacterial and plant ADP-glucose pyrophosphorylase subunits. Additionally, there are three regions which are considered signature patterns (ExPASy PROSITE database, documents PS00808-PS00810). The first two regions are N-terminal and have been proposed to be part of the allosteric and substrate-binding sites in the Escherichia coli enzyme. The third pattern corresponds to a conserved region in the central part of the enzymes.
In eukaryotic cells, mannose-1-phosphate guanyltransferase is involved in eariy steps of protein glycosylation. This enzyme participates in mannose metabolism, and its enzymatic products are channeled into glycdprotein synthesis. Mannose-1-phosphate guanyltransferase (MPG), also referred to as NDP-hexose pyrophosphorylase or GDP-mannose pyrophosphorylase B, catalyzes the conversion of GTP and xcex1-D-mannose 1-phosphate into diphosphate and CDP-ethanolamine. This enzyme is very similar to CDP-glucose pyrophosphorylase and may be involved in the regulation of cell cycle progression. A cDNA coding for MPG 1 was recently isolated from a Trichoderma reesei cDNA library (Kruszewska, J. S. et al. (1998) Curr. Genet. 33:445-500). The nucleotide sequence of the 1.6 kb cDNA revealed an ORF which encodes a protein of 364 amino acids. Sequence comparisons demonstrate that this protein shares 70% identity with the yeast Saccharomvces cerevisiae MPG 1 gene and 75% identity with the Schizosaccharomvces pombe gene. MPGs are conserved among diverse organisms. For example, recent genome sequencing projects have identified MPG homologs in the plant Arabidousis thaliana and thenematode Caenorhabditis elerans (SEQ ID NO:32 and SEQ ID NO:33, respectively).
Alterations in glycosylation are known to occur in a number of disorders and diseases such as carbohydrate-deficient glycoprotein syndromes (CDGSs). In the biochemical pathway upstream of MPG is an important enzyme called phosphomannomutase (PMM) which provides the mannose 1-phosphate required for the reaction catalyzed by MPG. PMM catalyzes the conversion of D-mannose 6-phosphate to D-mannose 1-phosphate and has been implicated in CDGSs. CDGSs are a group of hereditary multisystem disorders (Matthijs, G. et al. (1 997) Nat. Genet. 16:88-92). The clinical phenotype of most CDGSs is dominated by severe psychomotor and mental retardation, as well as blood coagulation abnormalities as seen in thrombosis, bleeding, or stroke-like episodes. The characteristic biochemical abnormality of CDGSs is the hypoglycosylation of glycoproteins. Depending on the type of CDGS, the carbohydrate side chains of glycoproteins are either truncated or completely missing from the protein core.
A new type of CDGS, designated as CDGS type 1B, has recently been described (Niehues, R. et al. (1998) Clin. Invest. 101:1414-1420). The clinical phenotype of this new disorder is fundamentally different from other types of CDGS in that no psychomotor or mental retardation is present. Instead, CDGS type 1B is a gastrointestinal disorder characterized by protein-losing enteropathy. Some patients who are affected with CDGS type 1B suffer from thrombosis and life-threatening bleeding. A deficiency of phosphomannose isomerase was identified as the most likely cause of this syndrome, and a therapy was developed in the form of oral administration of mannose (Niehues, supra). Mannose treatment can correct the clinical phenotype in CDGS type 1B. It is noteworthy that CDGS is the first inherited disorder in human metabolism that shows a decrease in available mannose. The above findings indicate that increasing blood mannose levels might correct some protein giycosylation deficiencies.
The discovery of new human transferase proteins and the polynucleotides encoding them satisfies a need in the art by providing new compositions which are useful in the diagnosis, prevention, and treatment of cancer, developmental disorders, gastrointestinal disorders, genetic disorders, immunological disorders, neurological disorders, reproductive disorders, and smooth muscle disorders.
The invention features substantially purified polypeptides, human transferase proteins, referred to collectively as xe2x80x9cTRNSFSxe2x80x9d and individually as xe2x80x9cTRNSFS-1,xe2x80x9d xe2x80x9cTRNSFS-2,xe2x80x9d xe2x80x9cTRNSFS-3,xe2x80x9d xe2x80x9cTRNSFS-4,xe2x80x9d xe2x80x9cTRNSFS-5,xe2x80x9d xe2x80x9cTRNSFS-6,xe2x80x9d xe2x80x9cTRNSFS-7,xe2x80x9d xe2x80x9cTRNSFS-8,xe2x80x9d xe2x80x9cTRNSFS-9,xe2x80x9d xe2x80x9cTRNSFS-10,xe2x80x9d xe2x80x9cTRNSFS-11,xe2x80x9d xe2x80x9cTRNSFS-12,xe2x80x9d xe2x80x9cTRNSFS-13,xe2x80x9d xe2x80x9cTRNSFS-14,xe2x80x9d and xe2x80x9cTRNSFS-15.xe2x80x9d In one aspect, the invention provides a substantially purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15 (SEQ ID NO:1-15), and fragments thereof.
The invention further provides a substantially purified variant having at least 90% amino acid identity to at least one of the amino acid sequences selected from the group consisting of SEQ ID NO:1-15 and fragments thereof. The invention also provides an isolated and purified polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-1 5 and fragments thereof. The invention also includes an isolated and purified polynuclebtide variant having at least 90% polynucleotide sequence identity to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof.
Additionally, the invention provides an isolated and purified polynucleotide which hybridizes under stringent conditions to the polynucleotide encoding the polypepptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof. The invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide encoding the polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof.
The invention also provides a method for detecting a polynucleotide in a sample containing nucleic acids, the method comprising the steps of (a) hybridizing the complement of the poiynucieotide sequence to at least one of the polynucleotides of the sample, thereby forming a hybridization complex; and (b) detecting the hybridization complex, wherein the presence of the hybridization complex correlates with the presence of a polynucleotide in the sample. In one aspect, the method further comprises amplifying the polynucleotide prior to hybridization.
The invention also provides an isolated and purified polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30 (SEQ ID NO:16-30), and fragments thereof. The invention further provides an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucieotide sequence selected from the group consisting of SEQ ID NO:16-30 and fragments thereof. The invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:16-30 and fragments thereof.
The invention further provides an expression vector containing at least a fragment of the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof. In another aspect, the expression vector is contained within a host cell.
The invention also provides a method for producing a polypeptide, the method comprising the steps of: (a) culturing the host cell containing an expression vector containing at least a fragment of a polynucleotide under conditions suitable for the expression of the polypeptide; and (b) recovering the polypeptide from the host cell culture.
The invention also provides a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
The invention further includes a purified antibody which binds to a polypeptide selected from the group consisting of SEQ ID NO:1-15 and fragments thereof. The invention also provides a purified agonist and a purified antagonist to the polypeptide.
The invention also provides a method for treating or preventing a disorder associated with decreased expression or activity of TRNSFS, the method comprising administering to a subject in need of such treatment an effective amount of a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
The invention also provides a method for treating or preventing a disorder associated with increased expression or activity of TRNSFS, the method comprising administering to a subject in need of such treatment an effective amount of an antagonist of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-15 and fragments thereof.